importGTF {IsoformSwitchAnalyzeR} | R Documentation

## Import Transcripts from a GTF file into R

### Description

Function for importing a GTF (can be either gziped or unpacked) into R as a `switchAnalyzeRlist`. This approach is well suited if you just want to annotate a transcriptome and are not interested in expression. If you are interested in expression estimates it is easier to use importRdata.

### Usage

    importGTF(
        pathToGTF,
        addAnnotatedORFs=TRUE,
        onlyConsiderFullORF=FALSE,
        removeNonConvensionalChr=FALSE,
        includeVersionIfAvailable=TRUE,
        PTCDistance=50,
        quiet=FALSE
    )

### Arguments

`pathToGTF` | A string indicating the full path to the (gziped or unpacked) GTF that should be imported.
`addAnnotatedORFs` | A logic indicating whether the ORF from the GTF should be added to the `switchAnalyzeRlist`. This ORF is defined as the regions annoated as 'CDS' in the 'type' collumn (collumn 3). Default is TRUE.
`onlyConsiderFullORF` | A logic indicating whether the ORFs added should only be added if they are fully annotated. Here fully annoated is defined as those that both have a annotated 'start_codon' and 'stop_codon' in the 'type' column (column 3). This argument is only considered if onlyConsiderFullORF=TRUE. Default is FALSE.
`removeNonConvensionalChr` | A logic indicating whether non-conventional chromosomes, here defined as chromosome names containing a '_'. These regions are typically used to annotate regions that cannot be assocaiated to a specific region (such as the human 'chr1_gl000191_random') or regions quite different due to different haplotypes (e.g. the 'chr6_cox_hap2'). Default is FALSE.
`includeVersionIfAvailable` | A logic indicateding whether to combined gene/transcript ids with their respective version numbers (GENCODE style) if the version numbers are in a seperate column - as is often the case with Ensemble data (this functionality will not remove exsiting version numbering from ids if set to FALSE). Defalut is TRUE
`PTCDistance` | Only considered if `addAnnotatedORFs=TRUE`. A numeric giving the premature termination codon-distance: The minimum distance from the annotated STOP to the final exon-exon junction, for a transcript to be marked as NMD-sensitive. Default is 50
`quiet` | A logic indicating whether to avoid printing progress messages. Default is FALSE

### Details

The GTF file must have the following 3 annotation in column 9: 'transcript_id', 'gene_id', and 'gene_name'. Furthermore if addAnnotatedORFs is to be used the 'type' column (column 3) must contain the features marked as 'CDS'. If the onlyConsiderFullORF argument should work the GTF must also have 'start_codon' and 'stop_codon' annoated in the 'type' column (column 3).

### Value

A `switchAnalyzeRlist` containing a all the gene and transcript information as well as the transcipt models. See ?switchAnalyzeRlist for more details.

If `addAnnotatedORFs=TRUE` a `data.frame` containing the details of the ORF analysis have been added to the switchAnalyzeRlist under the name 'orfAnalysis'.

The data.frame added have one row pr isoform and contains 11 columns:

- `isoform_id`: The name of the isoform analyzed. Mathces the 'isoform_id' entry in the 'isoformFeatures' entry of the switchAnalyzeRlist

- `orfTransciptStart`: The start position of the ORF in transcript cooridnats, here defined as the position of the 'A' in the 'AUG' start motif.

- `orfTransciptEnd`: The end position of the ORF in transcript coordinats, here defined as the last nucleotide before the STOP codon (meaning the stop codon is not included in these coordinates).

- `orfTransciptLength`: The length of the ORF

- `orfStarExon`: The exon in which the start codon is

- `orfEndExon`: The exon in which the stop codon is

- `orfStartGenomic`: The start position of the ORF in genomic cooridnats, here defined as the the position of the 'A' in the 'AUG' start motif.

- `orfEndGenomic`: The end position of the ORF in genomic coordinats, here defined as the last nucleotide before the STOP codon (meaning the stop codon is not included in these coordinates).

- `stopDistanceToLastJunction`: Distance from stop codon to the last exon-exon junction

- `stopIndex`: The index, counting from the last exon (which is 0), of which exon is the stop codon is in.

- `PTC`: A logic indicating whether the isoform is classified as having a Premature Termination Codon. This is defined as having a stop codon more than `PTCDistance` (default is 50) nt upstream of the last exon exon junciton.

NA means no information was advailable aka no ORF (passing the `minORFlength` filter) was found.

### Author(s)

Kristoffer Vitting-Seerup

### References

Vitting-Seerup et al. The Landscape of Isoform Switches in Human Cancers. Mol. Cancer Res. (2017).

### See Also

`createSwitchAnalyzeRlist`
`preFilter`

### Examples

    # Import exampled gtf file

    aSwitchList <- importGTF(pathToGTF=system.file("extdata/example.gtf.gz", package="IsoformSwitchAnalyzeR"))
    aSwitchList

[Package IsoformSwitchAnalyzeR version 1.4.0 Index]